From e7338a61f3ce96dadf44ac80b2b32cc5ba4b94c8 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Tue, 8 Mar 2022 20:39:47 +0000 Subject: [PATCH] JAL-3746 JAL-3841 new README and finalising 2.11.2.0 release notes --- README | 37 ++++++++++++++++--- help/help/html/releases.html | 82 ++++++++++++++++++++++++------------------ 2 files changed, 81 insertions(+), 38 deletions(-) diff --git a/README b/README index b374479..f121a93 100644 --- a/README +++ b/README @@ -1,5 +1,34 @@ -Please see doc/building.md for up to date build and running instructions for the Java desktop application. +Jalview README +============== -JalviewJS. -See README_GRADLE_JALVIEWJS-2019-10-22.md for build instructions for JalviewJS. -This is a little sparse but enough to do the transpilation. +Welcome ! + +Jalview is free (GPLv3 licensed) software for creation, interactive +visualisation and analysis of alignments of biological sequences. It +was developed by Michele Clamp in 1996, and now maintained by the +Jalview Development team in the Barton group at the University of +Dundee. + +If you'd like to help out please check out the website +(www.jalview.org) and get in touch. See CITATION for the canonical +reference if you need to cite Jalview. + +To build the Jalview Desktop application and JalviewJS, the JavaScript +transpiled version (with the help of java2script, courtesy of Bob +Hanson), you will need a Java 11 JDK and a recent version of +Gradle. For development we recommend Eclipse - you should be able to +import Jalview as a Gradle project with the Buildship plugin. + +Most likely you'll want to take a look at doc/building.md to find out +exactly what is needed. If you already have Java 11 and Gradle, then +the tldr: + +gradle test # run functional test suite + +gradle shadowJar # build a single executable Jar under build/lib/ + +gradle jalviewjs # builds JalviewJS under build/jalviewjs + +If you want to build JalviewJS then you will also need to download +Eclipse for your platform, since transpilation requires an Eclipse +plugin. diff --git a/help/help/html/releases.html b/help/help/html/releases.html index 2f9c096..e02d472 100755 --- a/help/help/html/releases.html +++ b/help/help/html/releases.html @@ -68,6 +68,10 @@ li:before { Chimera.
  • + Upgraded bundled version of Jmol + to 14.31.53 +
    • +
  • Discover 3D structure data for sequences with Uniprot references via 3D-Beacons
    • @@ -101,8 +105,9 @@ li:before {
  • Updated Ensembl REST Client compatibility - to 15.2 and revised model organism names (rat, xenopus, dmelanogaster now - rattus_norvegicus, xenopus_tropicalis, drosophila_melanogaster) + to 15.2 and revised model organism names (rat, xenopus, + dmelanogaster now rattus_norvegicus, xenopus_tropicalis, + drosophila_melanogaster)
  • Sequence IDs split on '_' as well as other @@ -145,8 +150,7 @@ li:before { GPL license info on splash screen and About text
    • - - Jalview Native App + Jalview Native App JalviewJS Development - JalviewJS - JalviewJS + - - Known Issues + Known Issues -- 1.7.10.2